Hi Doug,
probably something went wrong during the editing. E.g maybe you edited
files in the cross sectional or base directories and copied/saved these
to the longitudinals or vice-verca. There should be no mis-alignments.
I would recommend this:
1. run one such subjects without edits through
Hi Freesurferers
I appreciate if anyone could give me their thoughts on this question.
Thanks
Mona
Zahra (Mona) Nasiriavanaki
Postdoctoral Research Fellow
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129
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Hi all,
I ran a 2yo subject through FS6.0 using 'recon-all -i /firstdicom.dcm -all' and
the output segmentations and surfaces looks good.
Can someone explain why I see different alignments when I view the 001.mgz and
brainmask.mgz files in freeview,
Hi,
When you load brainmask.mgz as the second volume, it will be realigned
to 001.mgz. The default resample method is nearest-neighbor. Thus you
get the blocky look. You can try loading it with trilinear or cubic
resampling like this from the command-line:
freeview -v 001.mgz brainmask.mgz -
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Thanks for info.
If I open only the brainmsk.mgz only from a new terminal it is rotated and not
in its native orientation (which is 001's orientation).
Why does it not appear to be in native space in freeview?
Jim
From: freesurfer-boun...@nmr.mgh.ha
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Hey Martin,
Sounds like a logical approach. I'll give it a try and let you know how it ends
up.
I am using version 6.0 by the way.
Thanks,
Doug
-Original Message-
From: Martin Reuter
Sent: Monday, September 16, 2019 2:39 AM
To: Freesurfer
The first volume is always displayed in its original orientation where
pixel data are stored. So that the pixel data don't get resampled
(unless you force it with '-r' flag to resample it in standard RAS).
Ruopeng
On 9/16/19 1:06 PM, Alexopoulos, Dimitrios wrote:
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I'm still a little confused. When I open up the brainmask.mgz in freeview I see
the following. It is rotated compared to the native 001.mgz below.
[cid:image002.jpg@01D56C9C.9A38CF50]
I then open the 001.mgz with freeview in a NEW terminal (seperate
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To whom it may concern,
I am attempting to run the hippocampal and amygdala segmentation
(https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala)
on the development version of FreeSurfer. However, I am running into a couple
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Dear Freesurfer devs,
I tried to open the brainmask.mgz file in freeview but I obtained this
error:
mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz, -1): could
not open file
MRIread failed: Unable to read from
/usr/local/freesurfer/subj
Yes, these two volume are aligned. But they are sliced differently. When
you display a single volume alone in freeview, it is by default
displayed in its native slice orientation.
Ruopeng
On 9/16/19 3:39 PM, Alexopoulos, Dimitrios wrote:
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I’m still a litt
If you run:
ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz
What does it show?
Ruopeng
On 9/16/19 4:29 PM, Miguel Ángel Rivas Fernández wrote:
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Dear Freesurfer devs,
I tried to open the brainmask.mgz file in freeview but I obtained this
error:
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Dear Ruopeng,
I put that command in the freeview command console and this is the output
[FreeView] ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz
This is not a shell. Only freeview commands are supported. Type '-h' for
all the available com
Can you run the command in the command window that you start freeview?
Ruopeng
> On Sep 16, 2019, at 5:11 PM, Miguel Ángel Rivas Fernández
> wrote:
>
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>
>
> Dear Ruopeng,
>
> I put that command in the freeview command console and this is the ou
Not that I know of, it is pretty limited.
On 9/13/19 11:13 AM, Zeng,Victor (BIDMC - Psychiatry) wrote:
Hi all,
I know tkmedit has been deprecated, but we're thinking about using it just for
quality check purposes since we found that it is less resource intensive. We're
trying to load multip
You can use a PARCSFILE. Run aparcstats2table with --help to get more info
On 9/14/19 3:30 PM, vin rasa wrote:
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Dear Freesurfer experts,
Is there a shortcut to extract mean thickness(ThickAvg) and std (ThickStd) from
rh/lh.aparc.stats for let's say 4 structu
Are you trying to do a parametric analysis? See
https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastParametricModulation
On 9/13/19 11:08 AM, Nasiriavanaki, Zahra wrote:
Dear Freesurfer experts
Hi
I have a question about weighting different contrasts using mkcontrast-sess
commmand.
I have single s
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